multiple alignments

You may want to try a program called MAP. The C source file map.c
is available by anonymous ftp from cs.mtu.edu under directory pub/huang.
The MAP program computes a multiple global alignment of sequences using
iterative pairwise method. The underlying algorithm for aligning
two sequences computes a best overlapping alignment bewteen
two sequences without penalizing terminal gaps. In addition,
long internal gaps in short sequences are not heavily penalized.
So MAP is good at producing an alignment where there are long
terminal or internal gaps in some sequences. The MAP program is
designed in a space-efficient manner, so long sequences can be aligned.
The MAP program is written in C and runs under Unix systems on
Sun workstations and under DOS systems on PCs.
We think that the program is portable to many machines.
The MAP program is described in the following paper:
Xiaoqiu Huang, "On global sequence alignment", to appear in CABIOS.
Xiaoqiu Huang
Department of Computer Science
Michigan Technological University
Houghton, MI 49931